Math Biology Seminar: Dhananjay Bhaskar

  • Date: 03/02/2016
Dhananjay Bhaskar, UBC

University of British Columbia


Cell Sorting and Tissue Invasion using Computational Cell-based Models


Computational modelling frameworks like CHASTE (Cancer, Heart and Soft Tissue Environment) and CompuCell3D are widely used to develop multiscale simulations of complex biological systems. These frameworks integrate models of subcellular behaviour (e.g. cell cycle, cell polarity, cell division), models of interaction between cells and models of transport of nutrients/signals at the tissue scale. Each cell is represented using a cell-based model which describes geometry and rules governing the movement of cells. In order to compare two widely used cell-based models, namely cellular Potts model (implemented in CompuCell3D) and vertex dynamics model (implemented in CHASTE), we have developed an automated pipeline to perform parameter sweeps and gather statistical data for different cell sorting scenarios. Based on preliminary analysis of this data, we can critically assess the performance of Potts model and vertex dynamics model, implement new features to improve performance and suggest ways to calibrate each model. In this talk, I will describe the methodology used to analyze simulation data and challenges in simulation calibration. In part 2 of my talk, I will discuss an application of computational modelling to study tissue invasion using experimental data to calibrate simulation parameters.

Other Information: 

Location: ESB: 4127